The wide use of ZnO and CuO nanoparticles in research, medicine, industry, and other fields has raised concerns about their biosafety. It is therefore unavoidable to be discharged into the sewage treatment system. Due to the unique physical and chemical properties of ZnO NPs and CuO NPs, it may be toxic to the members of the microbial community and their growth and metabolism, which in turn affects the stable operation of sewage nitrogen removal. This study summarizes the toxicity mechanism of two typical metal oxide nanoparticles (ZnO NPs and CuO NPs) to nitrogen removal microorganisms in sewage treatment systems. Furthermore, the factors affecting the cytotoxicity of metal oxide nanoparticles (MONPs) are summarized. This review aims to provide a theoretical basis and support for the future mitigating and emergent treatment of the adverse effects of nanoparticles on sewage treatment systems.